title: HL-60 + 100 µM curcumin, biological replicate 1

city: Düsseldorf

first: Charlotte

last: Esser

state: NRW

address: Aufm Hennekamp 50

department: Immunologie

institute: IUF

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on human GeneChip U133 2A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner 2500A.

data_processing: Cel files were processed using RMA (affy-package, R2.0)

source_name: HL-60 cells treated for 24h with 100 µM curcumin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HL-60 cells were cultivated in RPMI medium with 10 % FCS, 1 % penecillin and 1 % streptavidin at 37°C and 5 % CO2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HL-60 cells were treated for 24h with the different substances in 5ml tissue flasks

tag: cell line

value: HL-60 promyelocytic leukemia cell line

tag: leukemia type by fab

tag: agent

value: curcumin


title: SGF3165_FLAG_MES4FLAG_EEMB_1 extraction0_array2

status: Public on May 19 2009

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: lab: Strome; short description: An mouse monoclonal antibody to FLAG obtained from SIGMA; used to ChIP MES-4; lot: 065K6236; catalog: SGF3165; company: Other; clonal: Monoclonal; purified: Protein A/G; antigen: DYKDDDDK; host: Mouse; species: C. elegans; target name: FLAG; aliases: SGF3165_FLAG; official name: SGF3165_FLAG;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Processed data are obtained using following parameters: genome version is WS180

label: Cy3 dye

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: SGF3165_FLAG_MES4FLAG_EEMB_1 channel_1

growth_protocol: Worm_embryo_growth_and_harvest_vSS1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 4 times on ice at the following settings: 30 sec; 20% power output; 0.7 duty cycle. Cell debris was removed by centrifuging at 13,000rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000rpm, 4?C for 1 minute to remove lipids.  Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS1. Protein A or G-coupled Dynal magnetic beads from 20 ul of slurry were washed 3 times in 1ml of 5mg/ml IgG-Free BSA in PBS (wash buffer). Beads were resuspended in 100ul of the wash buffer and rotated with 5ug of the appropriate antibody overnight at 4 oC. Beads were further washed 2 times in the wash buffer and resuspended in 30ul of the wash buffer. Before beginning IP, 5% of starting material of protein (3-6mg) was saved as "input" at -20 oC. The antibody-conjugated Dynal beads were mixed with 3-6mg of protein and nutated for 2hrs at 4 oC. After washing the beads, captured proteins were eluted by incubating beads in 300 ul of TE with 1% SDS and 250mM NaCl for 2 times 15 minutes at 65 oC. Samples were treated with proteinase K and reverse-crosslinked at 65 oC overnight. DNA was purified using Zymo DNA purification column and eluted in in 43ul dH2O. RNA was digest for 1 hour at 37 oC with RNase One (Promega). For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn:  http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

tag: strain

tag: developmental stage

value: embryo

tag: genotype

value: mes-4(bn73); bnIs15

tag: transgene

value: mes-3 promoter

tag: antibody

label: Cy5 dye

source_name: SGF3165_FLAG_MES4FLAG_EEMB_1 channel_2

value: SGF3165 FLAG


title: HL-60 + 100 µM curcumin, biological replicate 2

type: RNA

country: Germany

label: biotin

molecule: total RNA

organism: Homo sapiens


title: SGF3165_FLAG_MES4FLAG_EEMB_3 extraction2_array0

description:
channel ch1 is ChIP DNA; Antibody information listed below: lab: Strome; short description: An mouse monoclonal antibody to FLAG obtained from SIGMA; used to ChIP MES-4; lot: 065K6236; catalog: SGF3165; company: Other; clonal: Monoclonal; purified: Protein A/G; antigen: DYKDDDDK; host: Mouse; species: C. elegans; target name: FLAG; aliases: SGF3165_FLAG; official name: SGF3165_FLAG;
channel ch2 is input DNA;

This is a Dye Swap sample.

source_name: SGF3165_FLAG_MES4FLAG_EEMB_3 channel_1

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

source_name: SGF3165_FLAG_MES4FLAG_EEMB_3 channel_2


title: Ovarian tumor sample 169

status: Public on May 20 2009

city: Groningen

first: Rudolf

middle: Stephan Nicolaas

last: Fehrmann

state: Groningen

department: Gynecologic Oncology

country: Netherlands

institute: University Medical Center Groningen

description: Channel 1 in raw data file ; Characteristics: STATUS: 0 = end of follow-up or death unrelated to ovarian cancer ;  1 = death due to ovarian cancer FUMND: Months from primary surgery SAMPLE NR: Unique RNA reference number

hyb_protocol: Protocol is available at http://microarrays.nki.nl/download/protocols/Hybridization_oligo_array_ULS_labeling_of_aRNA_2005.pdf

scan_protocol: Arrays were scanned with the Affymetrix GMS428 scanner (Affymetrix, Santa Clara, CA) and expression values were calculated by BlueFuse software (BlueGnome, Cambridge, UK).

data_processing: raw data

source_name: Advanced stage serous ovarian cancer

label_protocol: All cRNA samples (1.5 µg) were labeled with ULS-Cy5 and ULS-Cy3 label (BIOKÉ, Leiden, the Netherlands).

growth_protocol: All tumor samples were flash frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA from tumor samples was pelleted through cesium chloride density gradient ultracentrifugation (Roche, Almere, the Netherlands). After total RNA samples had been given DNAse treatment (Megascript T7 kit, Ambion, Huntingdon, UK), they were checked for residual DNA using a dinucleotide primer set D11S875 specific for genomic DNA. mRNA was linearly amplified by in vitro transcription using T7 RNA polymerase (Megascript T7 kit, Ambion, Huntingdon, UK) [13]. Quality/integrity of total and amplified mRNA (cRNA) was checked by spectrophotometer analysis, UV 260/280 ratio > 1.8, and/or agarose gel electrophoresis.

treatment_protocol: All tumor samples were obtained at primary surgery prior to chemotherapy.

tag: assigned unique patient id

tag: status

tag: fumnd

tag: age

tag: sample nr


title: HL-60 + 10 nM TCDD, biological replicate 2

source_name: HL-60 cells treated for 24h with 10 nM TCDD

value: TCDD


title: Vaginal_E2_Donor1

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

country: USA

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 2.0 Plus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS1.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Vaginal tissue from subjects treated for 3 months with 17b-estradiol, delivered via a skin patch, at a dose of 0.05 mg/day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNAeasy purificition was performed according to the manufacturer's instructions

tag: Age

tag: BMI

tag: Ethnic Origin

value: White


title: JL00003_DPY26_N2_MXEMB_1 extraction0_array0

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: lab: Lieb; short description: Recombinant protein was cloned and expressed with Novagen's Pet30-EkLIC system. Rabbit polyclonal antibodies were produced at Covance Immunology Services. DNA encoding epitopes were cloned into pGEX-5X-2 vector (Amersham Biosciences) and used to affinity-purify antibodies.; catalog: Jason Lieb; company: Covance; clonal: Polyclonal; purified: Affinity; antigen: 740-1262; host: Rabbit; species: C. elegans; target id: dpy-26; target name: DPY-26; aliases: DPY26; official name: JL0004_DPY26;

data_processing: ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes. Processed data are obtained using following parameters: genome version is WS180

source_name: JL00003_DPY26_N2_MXEMB_1 [input DNA]

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSE1. Embryos were resuspended in FA buffer and dounced 30 times (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

value: wild type

source_name: JL00003_DPY26_N2_MXEMB_1 [ChIP DNA]


title: SGF3165_FLAG_MES4FLAG_EEMB_1 extraction0_array0


title: A. niger Glucose pH 6.0 rep 2

status: Public on May 18 2009

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

description: Part of a study of the response to three levels of ambient pH.

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: Data processed with R 2.5.1 according to the protocol of Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92. PMID: 18332432

label: Affymetrix standard

organism: Aspergillus niger

source_name: A. niger mycelium grown on a glucose medium at pH 6

label_protocol: Affymetrix standard

extract_protocol: Affymetrix standard

tag: Dispersed liquid culture grown at pH 6.0


title: A. niger Glucose pH 6.0 rep 3


title: A. niger Glucose pH 4.5 rep 2

source_name: A. niger mycelium grown on a glucose medium at pH 4.5

tag: Dispersed liquid culture grown at pH 4.5


title: A. niger Glucose pH 4.5 rep 3


title: A. niger Glucose pH 4.5 rep 1


title: HL-60 + 10 nM TCDD, biological replicate 1

tag: cell line

tag: leukemia type by fab


title: A. niger Glucose pH 2.5 rep 3

source_name: A. niger mycelium grown on a glucose medium at 2.5

tag: Dispersed liquid culture grown at pH 2.5


title: SGF3165_FLAG_MES4FLAG_EEMB_1 extraction0_array1

tag: strain

tag: developmental stage


title: A. niger Glucose pH 2.5 rep 1


title: A. niger Glucose pH 2.5 rep 2


title: A. niger Glucose pH 6.0 rep 1


title: R001

status: Public on Jul 01 2009

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: The subject had recovered from melioidosis

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Whole blood from patient who had recovered from melioidosis

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: Tempus Spin Isolation Kit

tag: Gender

value: F

tag: Ethnicity

value: Not Hispanic or Latino

tag: Race

value: Asian

tag: Illness

value: Control/Recovery

tag: Treatment

tag: Pathogen


title: X06426_Nsp_23

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix model 640 hybridization oven.

scan_protocol: Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner.

data_processing: Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time.  One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  For Chromosome X, the average of the 20 normal female samples was used.   Each probe set was mapped to the genome, NCBI assembly version 35, using annotation provided by the Affymetrix web site.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.  GLAD segments composed of < 8 probesets were merged with the neighboring segment with the most similar copy number.

source_name: ovary-met

label_protocol: Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 500ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005). The fluidics station model FS450 was used.

extract_protocol: A small piece of frozen tissue was removed from a sample of frozen tissue and incubated in a proteinase K digestion solution followed by cleanup using the Qiagen M48 robotics protocol.

tag: Secondary malignant neoplasm of the omentum; OMENTUM

value: INTRAPERITONEAL IMPLANT OF MALIGNANT MIXED MULLERIAN TUMOR OF OVARY, HETEROLOGOUS TYPE, WITH MULTIPLE INTRAPERITONEAL IMPLANTS, T3CNXM0, FIGO STAGE IIIC., >90


title: X06425_Nsp_22

tag: Secondary malignant neoplasm of the peritoneum; PARASPLENIC MASS

value: INTRAPERITONEAL IMPLANT OF POORLY DIFFERENTIATED ADENOCARCINOMA OF OVARY WITH PAPILLARY SEROUS FEATURES; MULTIPLE INTRAPERITONEAL IMPLANTS (PARASPLENIC MASS, PELVIC ORGANS, OMENTUM); T3CNXM0, FIGO STAGE IIIC., >90


title: X31830_Nsp_52

description: Ovary tumors were profiled for copy-number alterations

source_name: ovary-adeno

tag: Primary malignant neoplasm of ovary; HYSTERECTOMY

value: ENDOMETRIOID ADENOCARCINOMA OF BOTH OVARIES WITH INVOLVEMENT OF FALLOPIAN TUBES; NOTE: PATIENT HAS CONCURRENTLY RESECTED ENDOMETRIOID ADENOCARCINOMA OF ENDOMETRIUM.  ENDOMETRIOSIS OF OVARIES ALSO PRESENT, SUGGESTING PRECURSOR LESION FOR CARCINOMA; SUBMITTING SITE FAVORS INTERPRETATION AS SYNCHRONOUS, MULTIFOCAL PRIMARIES., 75-90


title: X41111_Nsp_56

tag: Secondary malignant neoplasm of liver; LIVER, SEGMENTAL RESECTION

value: METASTATIC PAPILLARY SEROUS ADENOCARCINOMA OF OVARY; PRIMARY TUMOR RESECTED ONE YEAR PREVIOUSLY, NO INFORMATION ON INITIAL TUMOR STAGING.  NOTE: DONOR TREATED WITH CHEMOTHERAPY PRIOR TO ACQUISITION OF CURRENT SAMPLE., 75-90


title: X33601_Nsp_54

tag: Primary malignant neoplasm of ovary; RADICAL HYSTERECTOMY & BILATERAL SALPINGO-OOPHORECTOMY

value: MULLERIAN MIXED TUMOR, PRIMARY IN OVARY, WITH CARCINOMATOUS AND SARCOMATOUS COMPONENTS (HOMOLOGOUS).  REGIONAL NODES NEGATIVE FOR TUMOR., >90


title: X02908_Nsp_9

tag: Secondary malignant neoplasm of connective and other soft tissues; METASTATIC ADENOCARCINOMA IN SOFT TISSUES OF PELVIS; CONCURRENT ADENOCARCINOMA OF OVARY AND ENDOMETRIUM; FAVOR OVARIAN PRIMARY., 75-90


title: X34318_Nsp_55

tag: Secondary malignant neoplasm of the omentum; OMENTUM, BIOPSY

value: METASTATIC ADENOCARCINOMA, FROM HYSTERECTOMY FOR ADENOCARCINOMA (ENDOMETRIOID AND SEROUS DIFFERENTIATION) OF OVARIES., 75-90


title: X31812_Nsp_51

tag: Secondary malignant neoplasm of the omentum; MALIGNANT MIXED MULLERIAN TUMOR, PRIMARY IN PERITONEAL CAVITY, WITH INVOLVEMENT OF OMENTUM., >90


title: X02907_Nsp_8

tag: Secondary malignant neoplasm of the omentum; METASTATIC PAPILLARY SEROUS (CYST)ADENOCARCINOMA, OMENTUM; CONCURRENT ADENOCARCINOMAS OF ENDOMETRIUM AND OVARY; FAVOR METASTATIC CARCINOMA FROM OVARY, >90


title: X31873_Nsp_53

tag: Primary malignant neoplasm of ovary; RADICAL HYSTERECTOMY

value: PAPILLARY SEROUS ADENOCARCINOMA OF OVARY, INVOLVING BOTH OVARIES, FALLOPIAN TUBE, PELVIC PERITONEUM, REGIONAL NODES (N1) , AND INGUINAL NODES (M1).  ER 10% POS, PR-, CA 125+., 75-90


title: X06425_Sty_22


title: X02908_Sty_9


title: X17989_Nsp_48

tag: Secondary malignant neoplasm of the omentum; OMENTECTOMY

value: METASTATIC PAPILLARY SEROUS ADENOCARCINOMA TAKEN AT BILATERAL SALPINGO-OOPHORECTOMY FOR PAPILLARY SEROUS CARCINOMA OF OVARY., 75-90


title: X06426_Sty_23


title: X18012_Nsp_49

tag: Secondary malignant neoplasm of the omentum; OMENTUM, EXCISION

value: METASTATIC ADENOCARCINOMA WITH PAPILLARY FEATURES, C/W METASTATIC PAPILLARY SEROUS CARCINOMA FROM OVARY., 75-90


title: X03310_Nsp_12

tag: Secondary malignant neoplasm of colon; METASTATIC ADENOCARCINOMA TO COLON, FROM PRIMARY PAPILLARY SEROUS ADENOCARCINOMA OF PERITONEUM., 75-90


title: X16780_Nsp_47

tag: Secondary malignant neoplasm of the peritoneum; CUL-DE-SAC/RECTOSIGMOID MASS EXCISION

value: MALIGNANT MULLERIAN MIXED TUMOR (MMMT), RECURRENT FROM OVARIAN PRIMARY 2.5 YEARS PREVIOUSLY; DONOR IS S/P RECENT AND LONG-TERM CHEMOTHERAPY., 75-90


title: X15848_Nsp_43

tag: Secondary malignant neoplasm of myometrium; MYOMETRIUM WITH MULLERIAN MIXED TUMOR FROM HYSTERECTOMY FOR MULLERIAN MIXED TUMOR WITH METASTASES TO OVARY AND OMENTUM., 75-90


title: X02907_Sty_8


title: X03310_Sty_12


title: X20796_Nsp_50

value: MALIGNANT MIXED MULLERIAN TUMOR OF OVARY,19 CM DIAMETER, W/ EXTENSIVE MICROSCOPIC DISSEMINATION IN ABDOMINAL CAVITY. CARCINOMATOUS COMPONENT:MIXED CLEAR CELL-ENDOMETRIOID TYPE. SARCOMATOUS COMPONENT:HIGH GRADE SPINDLE CELL SARCOMA., >90


title: X15355_Nsp_42

tag: Secondary malignant neoplasm of colon; COLONIC TISSUE WITH SEROSAL INVOLVEMENT BY RECURRENT PAPILLARY SEROUS ADENOCARCINOMA OF OVARY, 75-90


title: X16703_Nsp_44

value: METASTATIC PAPILLARY SEROUS ADENOCARCINOMA.  PATIENT WITH SEROUS ADENOCARCINOMA OF BILATERAL OVARIES., 75-90


title: X16719_Nsp_45

value: METASTATIC ADENOCARCINOMA, C/W OVARIAN PRIMARY.  OVARIAN ADENOCARCINOMA SHOWS PAPILLARY (GLGC REVIEW) AND ENDOMETRIOID DIFFERENTIATION., >90


title: X15133_Nsp_41

tag: Primary malignant neoplasm of ovary; RADICAL HYSTERECTOMY AND BILATERAL SALPINGO-OOPHORECTOMY

value: CLEAR CELL ADENOCARCINOMA OF OVARY WITH METASTASIS TO UTEROSACRAL LIGAMENT.  REGIONAL NODES NEGATIVE., 75-90


title: X43567_Nsp_57

tag: Primary malignant neoplasm of ovary; OVARY

value: MUCINOUS CYSTADENOCARCINOMA, 15 CM DIAMETER, 3639 GM, LIMITED TO OVARY WITH NO SURFACE IMPLANTS.  NO INFORMATION ON UTERUS OR OTHER OVARY; PERITONEAL BIOPSIES AND REGIONAL NODES NEGATIVE., 75-90


title: X16742_Nsp_46

tag: Secondary malignant neoplasm of the omentum; OMENTECTOMY FROM BSO/OMENTECTOMY

value: PAPILLARY SEROUS CARCINOMA, METASTATIC FROM OVARY.  NOTE: IN SITU CARCINOMA IS PRESENT IN THE FALLOPIAN TUBE, HOWEVER, DUE TO THE EXTENT OF OVARIAN INVOLVEMENT BY INVASIVE TUMOR (1.5 CM), CODED AS OVARIAN PRIMARY., 75-90


title: X43567_Sty_57


title: X31830_Sty_52

tag: Primary malignant neoplasm of ovary; HYSTERECTOMY


title: X41111_Sty_56

tag: Secondary malignant neoplasm of liver; LIVER, SEGMENTAL RESECTION


title: X15053_Nsp_40

tag: Secondary malignant neoplasm of the omentum; OMENTUM WITH EXTENSIVE MACROSCOPIC INVASIVE IMPLANTS OF CARCINOMA IN PATIENT WITH SEROUS PAPILLARY CARCINOMA OF BILATERAL OVARIES WITH IMPLANTS OF UTERINE SEROSA AND UNILATERAL PARAMETRIUM., 75-90


title: X31873_Sty_53


title: X16780_Sty_47


title: X20796_Sty_50


title: X12292_Nsp_36

value: PAPILLARY SEROUS ADENOCARCINOMA OF OVARY, HIGH GRADE, UNILATERAL, WITH SEROSAL IMPLANTS OF UTERUS, COLON, AND OMENTUM; REGIONAL NODES NEGATIVE., 75-90


title: X17989_Sty_48


title: X33601_Sty_54

tag: Primary malignant neoplasm of ovary; RADICAL HYSTERECTOMY & BILATERAL SALPINGO-OOPHORECTOMY


title: X12733_Nsp_37

tag: Secondary malignant neoplasm of the omentum; HYSTERECTOMY AND OMENTECTOMY

value: METASTATIC POORLY DIFFERENTIATED CARCINOMA (ORIGINATING SITE FAVORS ENDOMETRIOID SUBTYPE), C/W OVARIAN PRIMARY; INVOLVING BOTH OVARIES, PERITONEAL SURFACES, AND OMENTUM (MACROSCOPIC, T3C).  NO INFORMATION ON NODAL STATUS.  NOTE: DONOR TREATED WITH NEOADJUVANT CHEMOTHERAPY., >90


title: X31812_Sty_51

tag: Secondary malignant neoplasm of the omentum; MALIGNANT MIXED MULLERIAN TUMOR, PRIMARY IN PERITONEAL CAVITY, WITH INVOLVEMENT OF OMENTUM., >90


title: X34318_Sty_55

tag: Secondary malignant neoplasm of the omentum; OMENTUM, BIOPSY


title: X10197_Nsp_34

tag: Primary malignant neoplasm of ovary; RADICAL HYSTERECTOMY AND OOPHORECTOMY

value: BILATERAL PAPILLARY SEROUS ADENOCARCINOMA OF OVARY, WITH UNILATERAL SURFACE INVOLVEMENT; PERITONEAL SURFACES AND REGIONAL NODES NEGATIVE., >90


title: X18012_Sty_49


title: X16703_Sty_44

tag: Secondary malignant neoplasm of the omentum; OMENTECTOMY


title: X12788_Nsp_38

value: MACROSCOPIC (0.2 CM), METASTATIC PAPILLARY SEROUS CARCINOMA OF OVARY; NO INFORMATION ON REGIONAL NODE STATUS OR DISTANT METASTASES.  SUBSEQUENT IMPLANTS INVOLVING PELVIS AND SEROSA OF SMALL AND LARGE BOWEL BIOPSIED 6 MONTHS LATER., 75-90


title: X12004_Nsp_35

value: MALIGNANT MIXED MULLERIAN TUMOR, PRIMARY IN OVARY, INVOLVING BOTH OVARIES WITH WIDESPREAD INVOLVEMENT OF PERITONEAL SURFACES.  NO INFORMATION ON NODAL STATUS.  NOTE: DONOR TREATED WITH NEOADJUVANT CHEMOTHERAPY PRIOR TO ACQUISITION OF CURRENT SAMPLE., >90


title: X15355_Sty_42


title: X16742_Sty_46


title: X10181_Nsp_33

tag: Secondary malignant neoplasm of the omentum; OMENTUM

value: METASTATIC RECURRENT PAPILLARY SEROUS ADENOCARCINOMA OF OVARY.  NOTE: DONOR TREATED WITH CHEMOTHERAPY AT TIME OF INITIAL DIAGNOSIS 4 YEARS PRIOR., 75-90


title: X15848_Sty_43


title: X16719_Sty_45


title: X15133_Sty_41


title: X09098_Nsp_32

value: SEROUS CYSTADENOCARCINOMA, INVOLVING FALLOPIAN TUBE, PERITONEAL SURFACES, OMENTUM, AND REGIONAL LYMPH NODES., >90


title: X15050_Nsp_39

value: SEROUS PAPILLARY CARCINOMA WITH EXTENSIVE SURFACE INVOLVEMENT OF BILATERAL OVARIES, METASTASIS TO PERITONEAL SOFT TISSUE, INVOLVEMENT OF UNILATERAL PARAMETRIAL TISSUE, AND MICROSCOPIC INVASIVE IMPLANTS WITHIN OMENTUM., 75-90


title: X15050_Sty_39


title: X15053_Sty_40


title: X12292_Sty_36

tag: Primary malignant neoplasm of ovary; RADICAL HYSTERECTOMY


title: X08651_Nsp_31

value: SEROUS (CYST)ADENOCARCINOMA, INVOLVING BOTH OVARIES WITH MACROSCOPIC INTRAPERITONEAL SPREAD TO OMENTUM., 75-90


title: X12733_Sty_37


title: X10197_Sty_34


title: X12788_Sty_38


title: X09098_Sty_32


title: mediodorsal thalamus, left, biological rep1

city: New Haven

first: Matthew

middle: Bonser

last: Johnson

state: CT

address: 333 Cedar St., SHM C-316

department: Neurobiology

institute: Yale University School of Medicine

description: gene-level analysis

hyb_protocol: Samples were hybridized according to Affymetrix protocols

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Data were processed using Partek Genomics Suite. Core probesets were imported using RMA defaults with probe GC content correction

source_name: mediodorsal thalamus, left

label_protocol: Samples were treated with the RNeasy Mini Kit (Qiagen) to exclude smaller RNAs, and fragmented and labeled using the Affymetrix Whole Transcript Sense Target Labeling Assay.

growth_protocol: not applicable

extract_protocol: Samples were dissected from late 2nd trimester human brains obtained from the Albert Einstein College of Medicine Human Fetal Tissue Repository and total RNA isolated using TRIzol.

treatment_protocol: not applicable

tag: Age

value: 18 weeks gestation

tag: Post-Mortem Interval <1hr


title: X07915_Nsp_29

value: PAPILLARY SEROUS ADENOCARCINOMA, PRIMARY SITE UNKNOWN (C/W OVARY, OTHER MULLERIAN SITE, OR PRIMARY PERITONEAL CARCINOMATOSIS)., >90


title: X07525_Sty_26

value: PAPILLARY SEROUS ADENOCARCINOMA., >90


title: X07525_Nsp_26


title: X07756_Nsp_28

value: SEROUS ADENOCARCINOMA, ENDOMETRIOID TYPE PER SUBMITTED PATHOLOGY REPORT; GLGC PATH. REVIEW SHOWS ONLY SEROUS ADENOCARCINOMA., 75-90


title: X07556_Nsp_27

value: SEROUS CYSTADENOCARCINOMA., >90


title: X07556_Sty_27


title: X07918_Sty_30

value: METASTATIC PAPILLARY SEROUS ADENOCARCINOMA, PRIMARY IN OVARY (BOTH INVOLVED) WITH PERITONEAL CARCINOMATOSIS AND LYMPH NODE METASTASES., 75-90


title: X12004_Sty_35


title: X07915_Sty_29


title: X07473_Nsp_25

value: CLEAR CELL CARCNINOMA., >90


title: X06424_Sty_21

value: PERITONEAL IMPLANT OF POORLY DIFFERENTIATED ADENOCARCINOMA OF OVARY WITH PAPILLARY SEROUS FEATURES; MULTIPLE INTRAPERITONEAL IMPLANTS (PARASPLENIC MASS, PELVIC ORGANS, OMENTUM)., >90


title: X08651_Sty_31


title: X06427_Sty_24

value: MALIGNANT MIXED MULLERIAN TUMOR OF OVARY, HETEROLOGOUS TYPE, WITH MULTIPLE INTRAPERITONEAL IMPLANTS, T3CNXMX, FIGO STAGE IIIC., >90


title: X07756_Sty_28


title: X10181_Sty_33


title: X06427_Nsp_24


title: X06424_Nsp_21


title: X07918_Nsp_30


title: X07473_Sty_25


title: X06423_Nsp_20

value: PERITONEAL IMPLANT OF PAPILLARY SEROUS ADENOCARCINOMA OF OVARY; MULTIPLE INTRAPERITONEAL IMPLANTS ( INTESTINE, PELVIC ORGANS, OMENTUM)., 75-90


title: X04099_Nsp_15

value: OVARIAN PAPILLARY SEROUS CARCINOMA WITH FOCAL ENDOMETRIOID DIFFERENTIATION, INVOLVING OMENTUM, UTERINE SEROSA, AND RECTUM.  REGIONAL NODES NEGATIVE., >90


title: X06302_Nsp_18

tag: Primary malignant neoplasm of ovary; MALIGNANT MIXED MULLERIAN TUMOR, OVARY, >90


title: X04950_Nsp_17

tag: Secondary malignant neoplasm of the omentum; RADICAL HYSTERECTOMY AND OOPHORECTOMY

value: PAPILLARY SEROUS ADENOCARCINOMA OF OVARY WITH EXTENSIVE INTRAABDOMINAL SPREAD, INVOLVING OMENTUM. INITIAL STAGING BY SITE REPORTED AS STAGE 3C., 75-90


title: X06423_Sty_20


title: X03299_Nsp_11

tag: Primary malignant neoplasm of ovary; MIXED PAPILLARY SEROUS AND ENDOMETRIOID CYSTADENOCARCINOMA, OVARY, 75-90


title: X06304_Nsp_19

tag: Primary malignant neoplasm of ovary; PAPILLARY SEROUS ADENOCARCINOMA OF OVARY., >90


title: X03495_Nsp_13

tag: Primary malignant neoplasm of the omentum; PRIMARY PAPILLARY SEROUS ADENOCARCINOMA OF PERITONEUM, INVOLVING OMENTUM (CONSIDERED A PRIMARY SITE)., 75-90


title: X04051_Nsp_14

tag: Primary malignant neoplasm of ovary; CLEAR CELL CARCINOMA OF RIGHT OVARY WITH TUBULOPAPILLARY FEATURES.  DONOR ALSO HAS SYNCHRONOUS MUCINOUS CYSTADENOMA OF LEFT OVARY., 75-90


title: X02909_Nsp_10

tag: Primary malignant neoplasm of ovary; PAPILLARY SEROUS ADENOCARCINOMA, OVARY; CONCURRENT ENDOMETRIAL CARCINOMA; FAVOR PRIMARY CARCINOMA OF OVARY., >90


title: X02909_Sty_10


title: X04051_Sty_14


title: X03299_Sty_11


title: X04851_Nsp_16

tag: Primary malignant neoplasm of ovary; OVARY

value: PAPILLARY SEROUS ADENOCARCINOMA., 75-90


title: X06302_Sty_18


title: X06304_Sty_19


title: X04950_Sty_17


title: X02619_Nsp_6

tag: Primary malignant neoplasm of ovary; ENDOMETRIOID CARCINOMA OF OVARY., 75-90


title: X02435_Nsp_5

tag: Secondary malignant neoplasm of connective and other soft tissues; GRANULOSA CELL TUMOR IN SOFT TISSUES OF PELVIS; RECURRENT FROM PRIMARY OF OVARY.  NOTE

value: DONOR TREATED WITH CHEMOTHERAPY 7 YEARS PRIOR AT TIME OF FIRST RECURRENCE., >90


title: X04099_Sty_15


title: X03495_Sty_13


title: sptR isogenic mutant strain grown in human saliva to stationary phase replicate 3

status: Public on May 16 2009

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

description: group A Streptococcus grown in human saliva

hyb_protocol: Target was hybridized using Affymetrix protocl

scan_protocol: Chips were scanned using Affymetrix protocol

data_processing: Data was processed using Gene Chip Operating Software and analyzed using Partek Genomics Suite.

organism: Streptococcus sp. 'group A'

source_name: group A streptococcus grown in human saliva

label_protocol: cDNA was labeled using Affymetrix protocol

extract_protocol: RNA was extracted with Qiagen mini kit.  cDNA was created from RNA using Affymetrix protocol

tag: growth stage

value: stationary phase


title: sptR isogenic mutant strain grown in human saliva to stationary phase replicate 1

description: group A streptococus grown in human saliva to stationary phase


title: X02428_Nsp_4

tag: Primary malignant neoplasm of ovary; ADENOCARCINOMA OF OVARY WITH MUCINOUS, SEROUS AND ENDOMETRIOID FEATURES, >90


title: X02619_Sty_6


title: X02683_Sty_7

tag: Primary malignant neoplasm of ovary; PAPILLARY SEROUS CYSTADENOCARCINOMA, OVARY, 75-90


title: X02427_Sty_3

tag: Primary malignant neoplasm of ovary; PAPILLARY CYSTADENOCARCINOMA, OVARY WITH SEROUS AND ENDOMETRIOID FEATURES, >90


title: X02435_Sty_5


title: X04851_Sty_16


title: X02428_Sty_4


title: sptR isogenic mutant strain grown in human saliva to mid-exponential phase replicate 3

description: group A Streptococcus grown to mid-exponential phase

hyb_protocol: Hybridization was done according to Affymetrix protocol

scan_protocol: Scanning was done according to Affymetrix protocol

data_processing: Data was imported into GCOS and analyzed using Partek.

source_name: group A streptococcus grown to mid-exponential phase

label_protocol: cDNA labeling was done according to Affymetrix protocol

extract_protocol: RNA was extracted using a Qiagen RNeasy kit.  cDNA was created according to Affymetrix protocol.

value: mid-exponential phase


title: sptR isogenic mutant strain grown in human saliva to mid-exponential phase replicate 4


title: sptR isogenic mutant strain grown in human saliva to mid-exponential phase replicate 2

hyb_protocol: Hybridization was done according to Affymetrix protocol.

scan_protocol: Scan was done according to Affymetrix protocol.

data_processing: Data was processed using GeneChip operating software (GCOS).

source_name: group A Streptococcus grown in human saliva

label_protocol: Fragmented cDNA was labeled according to Affymetrix protocol.

extract_protocol: RNA was isolated using a Qiagen mini kit.

treatment_protocol: Group A Streptococcus was grown at 37º C in human saliva to mid-exponential phase.  2x volume of RNA protect (Qiagen) was added and cells were pelleted by centrifugation.  RNA was isolated using Qiagen RNeasy kit.  cDNA creation, labeling, and fragmentation were done according to Affymetrix protocol.


title: sptR isogenic mutant strain grown in human saliva to stationary phase replicate 4


title: Wild-type group A Streptococcus grown in human saliva to stationary phase replicate 4

description: Group A Streptococcus grown in human saliva

treatment_protocol: Group A Streptococcus was grown at 37º C in human saliva to stationary phase.  2x volume of RNA protect (Qiagen) was added and cells were pelleted by centrifugation.  RNA was isolated using Qiagen RNeasy kit.  cDNA creation, labeling, and fragmentation were done according to Affymetrix protocol.


title: sptR isogenic mutant strain grown in human saliva to mid-exponential phase replicate 1


title: Wild-type group A Streptococcus grown in human saliva to stationary phase replicate 3

source_name: Group A Streptococcus grown in human saliva


title: Wild-type group A Streptococcus grown in human saliva to stationary phase replicate 1


title: Wild-type group A Streptococcus strain grown in human saliva to mid-exponential phase replicate 1

description: group A Streptococcus grown in human saliva to mid-exponential phase


title: Wild-type group A Streptococcus grown in human saliva to stationary phase replicate 2


title: Wild-type group A Streptococcus strain grown in human saliva to mid-exponential phase replicate 2

source_name: Group A streptococcus grown in human saliva


title: Wild-type group A Streptococcus strain grown in human saliva to mid-exponential phase replicate 4


title: Wild-type group A Streptococcus strain grown in human saliva to mid-exponential phase replicate 3


title: X02426_Sty_2

tag: Primary malignant neoplasm of ovary; MUCINOUS CYSTADENOCARCINOMA OF OVARY WITH MICROINVASION., 75-90


title: X02426_Nsp_2


title: X02427_Nsp_3


title: X02424_Nsp_1

tag: Primary malignant neoplasm of ovary; PAPILLARY SEROUS ADENOCARCINOMA, OVARY, >90


title: DN T cells

city: Boston

first: Jose

middle: C

last: Crispin

address: 330 Brookline Ave, CLS-928

department: Medicine

institute: Beth Israel Deaconess Medical Center

hyb_protocol: Microarray experiments were performed at the Beth Israel Deaconess Medical Center (BIDMC) Genomics Core as previously described.

data_processing: Raw data were normalized using RMAExpress version 1.0 and analyzed using Nexus Expression version 1.0.  Low intensity probes were filtered when their expression value was <8.0 in 70% of the samples.

source_name: TCR-alpha/beta CD4- CD8- human T cells

label_protocol: cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) containing approximately 54,700 transcripts were carried out using standard protocols.

extract_protocol: Total RNA was isolated from sorted T cells using QIAGEN Rneasy kit

tag: cell type

value: TCR-alpha-beta+ CD25- T cells

tag: origin

value: freshly isolated from peripheral blood


title: U937 cells treated with ultrasound only

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with ultrasound (0.3 W/cm2 for 1 min; ultrasound only) and followed by incubation for 3 h at 37°C.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: phycoerythrin

source_name: Human lymphoma U937 cells

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: cell line

value: Human lymphoma U937 cells

tag: agent

value: ultrasound only


title: X02424_Sty_1


title: sptR isogenic mutant strain grown in human saliva to stationary phase replicate 2

description: group A Streptococcus in human saliva


title: U937 cells treated with the combination of Sonazoid and ultrasound

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min; Sonazoid + Ultrasound) and followed by incubation for 3 h at 37°C.


title: U937 cells treated with Sonazoid only

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with Sonazoid (0.05%; Sonazoid only) and followed by incubation for 3 h at 37°C.

value: Sonazoid only


title: CD4 T cells

scan_protocol: Microarray experiments were performed at the Beth Israel Deaconess Medical Center (BIDMC) Genomics Core as previously described.

source_name: TCR-alpha/beta CD4+ CD8- human T cells


title: X02683_Nsp_7


title: U937 cells (non-treatment; control)

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control).

value: non-treatment; control


title: BEAF Mbn2 cells replicate 2 - Set 2

status: Public on May 15 2009

city: Atlanta

first: Ashley

middle: M

last: Bushey

state: GA

address: 1510 Clifton Rd. RRC 1071B

department: Biology

institute: Emory University

description: BEAF ChIP-chip Mbn2 cells

hyb_protocol: performed by NimbleGen (http://www.nimblegen.com)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction.

organism: Drosophila melanogaster

source_name: BEAF ChIP DNA from Mbn2 cells

growth_protocol: Mbn2 cells were maintained in M3+BPYE media with 10% FCS

extract_protocol: ChIP DNA: Chromatin immunoprecipitation was performed with 3-5x107 cells at ~80% confluency.  Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched by adding glycine to a final concentration of 0.125M.  Nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody overnight at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA isolated by phenol/chloroform extraction and EtOH precipitation.  DNA was amplified using using the GenomePlex Complete Whole Genome Amplification kit (Sigma WGA2) to obtain a sufficient amount of DNA.  Input DNA: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched by adding glycine to a final concentration of 0.125M.  Nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with Srotein A Sepharose beads.  Crosslinking was reversed and DNA was isolated by phenol/chloroform extraction and EtOH precipitation.  DNA was amplified using using the GenomePlex Complete Whole Genome Amplification kit (Sigma WGA2).

tag: cells

tag: antibody

value: BEAF

source_name: Input DNA from Mbn2 cells

value: Input DNA (no antibody)


title: CD8 T cells

source_name: TCR-alpha/beta CD4- CD8+ human T cells


title: CP190 Kc cells replicate 3 - Set 2

description: CP190 ChIP-chip Kc cells

scan_protocol: performed by NimbleGen (http://www.nimblegen.com)

source_name: CP190 ChIP DNA from Kc cells

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media

extract_protocol: ChIP DNA: Chromatin immunoprecipitation was performed with 3-5x107 cells at ~80% confluency.  Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched by adding glycine to a final concentration of 0.125M.  Nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody overnight at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA isolated by phenol/chloroform extraction and EtOH precipitation.  DNA was amplified using using the GenomePlex Complete Whole Genome Amplification kit (Sigma WGA2) to obtain a sufficient amount of DNA.  Input DNA: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched by adding glycine to a final concentration of 0.125M.  Nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with Protein A Sepharose beads.  Crosslinking was reversed and DNA was isolated by phenol/chloroform extraction and EtOH precipitation.  DNA was amplified using using the GenomePlex Complete Whole Genome Amplification kit (Sigma WGA2).

value: Kc

source_name: Input DNA from Kc cells


title: BEAF Mbn2 cells replicate 1 - Set 2

description: BEAF ChIP-chip Mbn2 cells

label_protocol: performed by NimbleGen (http://www.nimblegen.com)


title: dCTCF Mbn2 cells replicate 3 - Set 2

description: dCTCF ChIP-chip Mbn2 cells

source_name: dCTCF ChIP DNA from Mbn2 cells

value: dCTCF


title: dCTCF Mbn2 cells replicate 1 - Set 2

description: dCTCF ChIP-chip Mbn2 cells


title: snif1 knock-out mutant vs snif1 ade16 ade17 knock-out mutant (dye swap)

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Technical replicate 2 of 2 (dye swap).

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dried and ready for scanning.

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

organism: Saccharomyces cerevisiae

source_name: Total RNA extracted from snif1 knock-out mutant strain labeled with Cyanine-5 (red).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cell growth 24 hours at 30°C in SD medium (Casaminoacid 0.2%, Adenin 300µM, Uracil 200µM, Tryptophan 200µM) to an OD = 0.5

extract_protocol: Hot phenol extract procedure followed by RNEasy Mini Kit purification step (Quiagen)

tag: snif1 knock-out mat alpha snif1

value: :KanMX4 his3D1 leu2D0 ura3D0 strain

source_name: Total RNA extracted from snif1 ade16 ade17 knock-out mutant strain labeled with Cyanine-3 (green).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

tag: snif1 ade16 ade17 knock-out mat alpha snif1

value: :KanMX4 ade16::KanMX4 ade17::KanMX4 his3D1 leu2D0 ura3D0 strain


title: CP190 Mbn2 cells replicate 1 - Set 2

description: CP190 ChIP-chip Mbn2 cells

source_name: CP190 ChIP DNA from Mbn2 cells


title: BEAF Kc cells replicate 2 - Set 2

description: BEAF ChIP-chip Kc cells

source_name: BEAF ChIP DNA from Kc cells


title: CP190 Mbn2 cells replicate 2 - Set 2

description: CP190 ChIP-chip Mbn2 cells


title: dCTCF Kc cells replicate 2 - Set 2

description: dCTCF ChIP-chip Kc cells

source_name: dCTCF ChIP DNA from Kc cells


title: Su(Hw) Kc cells replicate 3 - Set 2

description: Su(Hw) ChIP-chip Kc cells

source_name: Su(Hw) ChIP DNA from Kc cells

value: Su(Hw)


title: BEAF Kc cells replicate 1 - Set 2

description: BEAF ChIP-chip Kc cells


title: dCTCF Mbn2 cells replicate 2 - Set 2

description: dCTCF ChIP-chip Mbn2 cells


title: CP190 Kc cells replicate 1 - Set 2

description: CP190 ChIP-chip Kc cells


title: Su(Hw) Mbn2 cells replicate 3 - Set 2

description: Su(Hw) ChIP-chip Mbn2 cells

source_name: Su(Hw) ChIP DNA from Mbn2 cells


title: snif ade16 ade17 knock-out mutant vs snif1 knock-out mutant

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from snif1 ade16 ade17 knock-out mutant strain labeled with Cyanine-5 (red).

source_name: Total RNA extracted from snif1 knock-out mutant strain labeled with Cyanine-3 (green).


title: Su(Hw) Mbn2 cells replicate 2 - Set 2

description: Su(Hw) ChIP-chip Mbn2 cells


title: CP190 Mbn2 cells replicate 3 - Set 2

description: CP190 ChIP-chip Mbn2 cells


title: Su(Hw) Mbn2 cells replicate 1 - Set 2

description: Su(Hw) ChIP-chip Mbn2 cells


title: dCTCF Kc cells replicate 1 - Set 2

description: dCTCF ChIP-chip Kc cells


title: dCTCF Kc cells replicate 3 - Set 2

description: dCTCF ChIP-chip Kc cells


title: Su(Hw) Kc cells replicate 1 - Set 2

description: Su(Hw) ChIP-chip Kc cells


title: CP190 Kc cells replicate 2 - Set 2

description: CP190 ChIP-chip Kc cells


title: pho4 knock-out mutant vs pho4 ade16 ade17 knock-out mutant (dye swap)

description: Technical replicate 2 of 2 (dye swap).

source_name: Total RNA extracted from pho4 knock-out mutant strain labeled with Cyanine-5 (red).

tag: pho2 knock-out mat alpha pho4

source_name: Total RNA extracted from pho4 ade16 ade17 knock-out mutant strain labeled with Cyanine-3 (green).

tag: pho4 ade16 ade17 knock-out mat alpha pho4


title: pho4 ade16 ade17 knock-out mutant vs pho4 knock-out mutant

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from pho4 ade16 ade17 knock-out mutant strain labeled with Cyanine-5 (red).

source_name: Total RNA extracted from pho4 knock-out mutant strain labeled with Cyanine-3 (green).

tag: pho4 knock-out mat alpha pho4


title: pho2ade16ade17 knock-out mutant vs pho2 knock-out mutant

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from pho2 ade16 ade17 knock-out mutant strain labeled with Cyanine-5 (red).

tag: pho2 ade16 ade17 knock-out mat alpha pho2

value: :KanMX4 ade16::KanMX4 ade17::KanMX4 his3D1 leu2D0 ura3D0 met17D0 strain

source_name: Total RNA extracted from pho2 knock-out in mutant strain labeled with Cyanine-3 (green).

tag: pho2 knock-out mat alpha pho2


title: pho2 knock-out mutant vs pho2 ade16 ade17 knock-out mutant (dye swap)

description: Technical replicate 2 of 2 (dye swap).

source_name: Total RNA extracted from pho2 knock-out mutant strain labeled with Cyanine-5 (red).

value: :KanMX4 his3D1 leu2D0 ura3D0 met17D0 strain

source_name: Total RNA extracted from pho2ade16ade17 knock-out mutant strain labeled with Cyanine-3 (green).


title: PKGI KO vs. WT brown adipose tissues replicate 3

city: Bonn

last: Mayer

address: Kurt-Georg-Kiesinger-Allee

institute: Fed. Inst. for Drugs and Med. Devices

description: all steps according to manufacturer's recommendations

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: DNA microarray scanner (Agilent)

data_processing: Agilent Feature Extraction Software default lowess normalization

organism: Mus musculus

source_name: WT

label_protocol: Agilent Low RNA Input Linear Amp Kit

extract_protocol: Trizol

tag: tissue

value: brown adipose

tag: genotype

value: WT

tag: genetic background

source_name: PKGI KO

value: PKGI KO


title: BEAF Mbn2 cells replicate 2 - Set 1

description: BEAF ChIP-chip Mbn2 cells

source_name: BEAF ChIP DNA from Mbn2 cells

source_name: Input DNA from Mbn2 cells


title: PKGI KO vs. WT brown adipocytes replicate 3

value: brown adipocytes


title: ade13-42 knock-out mutant vs WT

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from ade13-42 knock-out mutant strain labeled with Cyanine-5 (red).

tag: ade13-42 knock-out Mat alpha ade13-42 leu2-3, 112 lys2D201 ura3-52 strain

source_name: Total RNA extracted from WT strain labeled with Cyanine-3 (green).

tag: WT Mat alpha leu2-3, 112 lys2D201 ura3-52 strain


title: PKGI KO vs. WT brown adipocytes replicate 2

tag: cell type


title: CP190 Mbn2 cells replicate 2 - Set 1

description: CP190 ChIP-chip Mbn2 cells

source_name: CP190 ChIP DNA from Mbn2 cells


title: CP190 Mbn2 cells replicate 3 - Set 1

description: CP190 ChIP-chip Mbn2 cells


title: Su(Hw) Mbn2 cells replicate 3 - Set 1

description: Su(Hw) ChIP-chip Mbn2 cells

source_name: Su(Hw) ChIP DNA from Mbn2 cells


title: WT colon rep2

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 , and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome custom arrays (platform acc# GPL7173). Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

source_name: colon

label_protocol: 400ng of RNA was amplified and labeled using the One-Color Agilent Low RNA  Input Linear Amplification Kit

extract_protocol: Total RNA was extracted using Trizol reagent followed by a Qiagen RNEasy cleanup column. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer

tag: FVB/N


title: WT vs ade13-42 knock-out (dye swap)

description: Technical replicate 2 of 2 (dye swap).

source_name: Total RNA extracted from WT strain labeled with Cyanine-5 (red).

source_name: Total RNA extracted from ade13-42 knock-out mutant strain labeled with Cyanine-3 (green).


title: CP190 Mbn2 cells replicate 1 - Set 1

description: CP190 ChIP-chip Mbn2 cells


title: dCTCF Mbn2 cells replicate 1 - Set 1

description: dCTCF ChIP-chip Mbn2 cells

source_name: dCTCF ChIP DNA from Mbn2 cells


title: WT colon rep1


title: Su(Hw) Mbn2 cells replicate 2 - Set 1

description: Su(Hw) ChIP-chip Mbn2 cells


title: AGR2 KO colon rep 2


title: Su(Hw) Mbn2 cells replicate 1 - Set 1

description: Su(Hw) ChIP-chip Mbn2 cells


title: BEAF Kc cells replicate 2 - Set 1

description: BEAF ChIP-chip Kc cells

source_name: BEAF ChIP DNA from Kc cells

source_name: Input DNA from Kc cells


title: dCTCF Mbn2 cells replicate 3 - Set 1

description: dCTCF ChIP-chip Mbn2 cells


title: WT small intestine rep 4

source_name: small intestine


title: AGR2 KO colon rep 1


title: PKGI KO vs. WT brown adipose tissues replicate 2


title: CP190 Kc cells replicate 3 - Set 1

description: CP190 ChIP-chip Kc cells

source_name: CP190 ChIP DNA from Kc cells


title: dCTCF Mbn2 cells replicate 2 - Set 1

description: dCTCF ChIP-chip Mbn2 cells


title: Su(Hw) Kc cells replicate 2 - Set 2

description: Su(Hw) ChIP-chip Kc cells

source_name: Su(Hw) ChIP DNA from Kc cells


title: CP190 Kc cells replicate 2 - Set 1

description: CP190 ChIP-chip Kc cells


title: BEAF Kc cells replicate 1 - Set 1

description: BEAF ChIP-chip Kc cells


title: WT small intestine rep 3


title: WT small intestine rep 1


title: WT small intestine rep 2


title: BEAF Mbn2 cells replicate 1 - Set 1

description: BEAF ChIP-chip Mbn2 cells


title: AGR2 KO small intestine rep1


title: AGR2 KO small intestine rep4


title: dCTCF Kc cells replicate 3 - Set 1

description: dCTCF ChIP-chip Kc cells

source_name: dCTCF ChIP DNA from Kc cells


title: AGR2 KO small intestine rep2


title: AGR2 KO small intestine rep3


title: CP190 Kc cells replicate 1 - Set 1

description: CP190 ChIP-chip Kc cells


title: dCTCF Kc cells replicate 1 - Set 1

description: dCTCF ChIP-chip Kc cells


title: Su(Hw) Kc cells replicate 3 - Set 1

description: Su(Hw) ChIP-chip Kc cells


title: dCTCF Kc cells replicate 2 - Set 1

description: dCTCF ChIP-chip Kc cells


title: BEAF Mbn2 cells replicate 2 - Set 3

description: BEAF ChIP-chip Mbn2 cells


title: Su(Hw) Kc cells replicate 2 - Set 1

description: Su(Hw) ChIP-chip Kc cells


title: BEAF Mbn2 cells replicate 1 - Set 3

description: BEAF ChIP-chip Mbn2 cells


title: Su(Hw) Kc cells replicate 1 - Set 1

description: Su(Hw) ChIP-chip Kc cells


title: CP190 Mbn2 cells replicate 3 - Set 3

description: CP190 ChIP-chip Mbn2 cells


title: CP190 Mbn2 cells replicate 2 - Set 3

description: CP190 ChIP-chip Mbn2 cells


title: CP190 Mbn2 cells replicate 1 - Set 3

description: CP190 ChIP-chip Mbn2 cells


title: Kras_3m_rep2

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Gene expression data.
Replicate 2 of 2.

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor with RMA method.

source_name: ovary from 3-month-old Kras mutant mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

value: ovary

value: Kras (G12D) f/+; AMHR2-CRE

tag: age

value: 3 months


title: BEAF Kc cells replicate 1 - Set 3

description: BEAF ChIP-chip Kc cells

tag: cells


title: Kras_3m_rep1

description:
Gene expression data.
Replicate 1 of 2.


title: Su(Hw) Mbn2 cells replicate 2 - Set 3

description: Su(Hw) ChIP-chip Mbn2 cells

tag: antibody


title: dCTCF Mbn2 cells replicate 2 - Set 3

description: dCTCF ChIP-chip Mbn2 cells


title: dCTCF Mbn2 cells replicate 1 - Set 3

description: dCTCF ChIP-chip Mbn2 cells


title: dCTCF Mbn2 cells replicate 3 - Set 3

description: dCTCF ChIP-chip Mbn2 cells


title: Su(Hw) Mbn2 cells replicate 1 - Set 3

description: Su(Hw) ChIP-chip Mbn2 cells


title: CP190 Kc cells replicate 2 - Set 3

description: CP190 ChIP-chip Kc cells


title: Kras_d26_rep1

description:
Gene expression data.
Replicate 1 of 2.

source_name: ovary from 26-day-old Kras mutant mice

value: 26 days


title: CP190 Kc cells replicate 3 - Set 3

description: CP190 ChIP-chip Kc cells


title: BEAF Kc cells replicate 2 - Set 3

description: BEAF ChIP-chip Kc cells

value: BEAF


title: Su(Hw) Mbn2 cells replicate 3 - Set 3

description: Su(Hw) ChIP-chip Mbn2 cells

source_name: Input DNA from Mbn2 cells

value: Input DNA (no antibody)


title: CP190 Kc cells replicate 1 - Set 3

description: CP190 ChIP-chip Kc cells

value: Kc


title: Mbn2_Expression_Rep2

description: RNA expression data from cultured Mbn2 cells

data_processing: Normalized expression values were generated using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249).

source_name: Mbn2 cells

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.  Mbn2 cells were maintained in M3+BPYE media with 10% FCS.

extract_protocol: RNA was purified from Kc cell and Mbn2 cells with RNeasy kit (Qiagen) and cDNA synthesis was performed with High-Capacity cDNA Reverse Transctipion kit (Applied Biosystems).  DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Cells were not treated.


title: Kc_Expression_Rep2

description: RNA expression data from cultured Kc cells

source_name: Kc cells


title: HSC_LRC_Rep2

city: Heidelberg

first: Andreas

last: Trumpp

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

institute: Deutsches Krebsforschungszentrum (DKFZ)

description: Murine LRC HSC Replicate 2

hyb_protocol: Hybridization performed on a Affymetrix Fluidics Station

scan_protocol: Array scanning and raw data processing were done using GCOS software (Affymetrix)

data_processing: Data processing was performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Data was normalized using RMA.

label: Biotin label

source_name: Bone Marrow sorted for LRC: CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP+ HSCs

label_protocol: Biotin labelling of cRNA was performed utilizing the Affymetrix GeneChip IVT labelling kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from bone marrow sorted for LRC: CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP+ HSCs, using the PicoPure RNA kit (Arcturus, Menlo Park, CA). Per condition 3 independent samples were analysed. Two rounds of amplification for each RNA sample were performed utilizing the Nugen WT-Ovation Pico RNA Amplification System (Nugen, San Carlos, CA, USA).

tag: strain

value: SCL-tTA H2B-GFP transgenic mouse line that expresses the fusion protein histone H2B green fluorescent protein (H2B-GFP) under the control of a tetracycline responsive regulatory element, with the expression of the tTA-S2 transactivator under the control of the endogenous scl locus (SCL-tTA) limiting expression of GFP to both early embryonic and adult HSC/progenitor cells.

value: Bone Marrow sorted for LRC:CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP+ HSCs.

tag: timepoint

value: After 170 day chase (+ doxycycline)


title: HSC_non-LRC_Rep3

description: Murine non-LRC HSC Replicate 3

source_name: Bone Marrow sorted for non-LRC CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP Neg HSCs

extract_protocol: Total RNA was isolated from bone marrow sorted for non-LRC CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP Neg HSCs, using the PicoPure RNA kit (Arcturus, Menlo Park, CA). Per condition 3 independent samples were analysed. Two rounds of amplification for each RNA sample were performed utilizing the Nugen WT-Ovation Pico RNA Amplification System (Nugen, San Carlos, CA, USA).


title: Ag-Mo-WG-G4122A: hyb 409

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Transcriptome analysis of smooth muscle cells in atherosclerosis-prone and atherosclerosis-resistant regions of the aorta of apoE-/- mice at the age of 4 months

hyb_protocol: For Cy3 12pmol and for Cy5 8 pmol incorporated dye was fragmented and resuspended in 500 ml hybridization solution (Agilent).The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 60ºC, rpm=5 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) and images were processed with the Feature Extraction Software version 9.1.1.1 (Agilent).

data_processing: Log-ratio of Cy5/Cy3 of the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.1.1.1) were used for the data analysis. In case of duplicate probes for the same gene, log-ratios were averaged.

source_name: prone: aorta_arch_EKO_pool_6

label_protocol: Reagents: (1) RNase Out 40U/ul (Invitrogen, 5000U, Cat. No. 10777-019),(2) Random nonamers N9 1 ug/ul (Genset, 1862270), (3) 5 x first strand buffer (SuperScript II RT, Invitrogen, Cat. No. 18064-014), (4) 0.1 M DTT (SuperScript II RT, Invitrogen, Cat. No. 18064-014), (5) 10 mM dNTP/2 mM dCTP (Amersham Pharmacia Biotech, 100 mM, Cat. No. 272050/60/70/80), (6) CyTM-3-dCTP and CyTM-5-dCTP for microarrays (Amersham Pharmacia Biotech, 25 nmol, Cat. No. PA 53021 and PA 55021), (7) SuperScript II RT 200U/ul (Invitrogen, 10000U, Cat. No. 18064-014), (8) 2.5 M NaOH (Sigma, Cat. No. S-0899), (9) MOPS (3-(N-Morpholino)propanesulfonic acid) (Sigma, Cat. No. M-8899), (10) NaAc 3M, pH 5.0 (Sigma, Cat. No. S-2889), (11) QIAquick PCR Purification Kit (Qiagen, Cat. No 28106).  Cy5 Labeling Protocol: (1) Mix 5 ug of RNA from IVT (8 ul), 0.5 ul of RNase Out 40U/ul, 5 ul spikes (not for Arabidopsis thaliana) and 2 ul of random nonamers N9 1 ug/ul. (2) Denaturate at 70C for 10 minutes, chill on ice and add the following components: 4 ul of first strand buffer, 1 ul of 10 mM dNTP/2 mM dCTP, 2 ul of 0.1 M DTT, 1.5 ul of Cy5 dCTP and 1 ul of SuperScript II RT 200U/ul. (3) Incubate at 42C for 2.5 hours and then go to 4C or chill on ice. (4) Denaturate the RNA template by adding 2 ul of 2.5 M NaOH, incubating at 37C for exactly 15 minutes, adding 10 ul of 2 M MOPS and putting on ice. (5) Purification with QIAquick PCR Purification Kit according to manufacturers guidelines.

extract_protocol: Aorta were perfused with triton X-100 to remove endothelial cells. Aorta then divided into aortic arch (AA: aortic root, aortic arch, proximal 2 mm of thoracic aorta) and central thoracic aorta (TA: 6 mm distal from the proximal 2mm of the thoracic aorta).Aorta segments were immediately cut into small pieces and lysed in 350 µL Trizol reagent (Invitrogen, Merelbeke, Belgium). Subsequently, RNA was purified using the RNeasy MinElute kit (Qiagen, Antwerp, Belgium) and collected in 25 µL. RNA quality was tested by electrophoresis using the Agilent Bioanalyser. All RNA samples had a RNA integrity number (RIN) between 7.5 and 7.7. RNA extracts (12 µl) from the 6 mice were pooled and used for the microarray analysis.

tag: Strain

value: apoE-/-; 3 males, 3 females; age:16 weeks; tissue:aorta

source_name: resistant: thoracic_aorta_EKO_pool_6

label_protocol: Reagents:(1) RNase Out 40U/ul (Invitrogen, 5000U, Cat. No. 10777-019), (2) Random nonamers N9 1 ug/ul (Genset, 1862270), (3) 5 x first strand buffer (SuperScript II RT, Invitrogen, Cat. No. 18064-014), (4) 0.1 M DTT (SuperScript II RT, Invitrogen, Cat. No. 18064-014), (5) 10 mM dNTP/2 mM dCTP (Amersham Pharmacia Biotech, 100 mM, Cat. No. 272050/60/70/80), (6) CyTM-3-dCTP and CyTM-5-dCTP for microarrays (Amersham Pharmacia Biotech, 25 nmol, Cat. No. PA 53021 and PA 55021), (7) SuperScript II RT 200U/ul (Invitrogen, 10000U, Cat. No. 18064-014), (8) 2.5 M NaOH (Sigma, Cat. No. S-0899), (9) MOPS (3-(N-Morpholino)propanesulfonic acid) (Sigma, Cat. No. M-8899), (10) NaAc 3M, pH 5.0 (Sigma, Cat. No. S-2889), (11) QIAquick PCR Purification Kit (Qiagen, Cat. No 28106).   Cy3 labeling Protocol: (1) Mix 5 ug of RNA from IVT (8 ul), 0.5 ul of RNase Out 40U/ul, 5 ul spikes (not for Arabidopsis thaliana) and 2 ul of random nonamers N9 1 ug/ul. (2) Denaturate at 70C for 10 minutes, chill on ice and add the following components: 4 ul of first strand buffer, 1 ul of 10 mM dNTP/2 mM dCTP, 2 ul of 0.1 M DTT, 1.5 ul Cy3 dCTP and 1 ul of SuperScript II RT 200U/ul. (3) Incubate at 42C for 2.5 hours and then go to 4C or chill on ice. (4) Denaturate the RNA template by adding 2 ul of 2.5 M NaOH, incubating at 37C for exactly 15 minutes, adding 10 ul of 2 M MOPS and putting on ice. (5) Purification with QIAquick PCR Purification Kit according to manufacturers guidelines.


title: HSC_LRC_Rep1

description: Murine LRC HSC Replicate 1

value: Bone Marrow sorted for LRC:CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP+ HSCs


title: CDC2171

first: Brian

middle: H

last: Raphael

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

description: GFF file shows signal intensities for both channels.

hyb_protocol: Arrays were cohybridized with both Cy3-labeled DNA (test strain) and Cy5-labeled DNA (reference strain) for 14 hrs. at 42C.

scan_protocol: GenePix 4000B using 532 nm and 635 nm

data_processing: Signal intensities were extracted and normalized log2 ratio data were determined using Nimblescan ver 2.3 (Nimblegen, Madison, WI).

organism: Clostridium botulinum

label_protocol: 1 ug of genomic DNA was labeled with Cy3 random primers and Klenow fragment

extract_protocol: Epicenter MasterPure DNA purification Kit (Madison, WI)

tag: toxin subtype

source_name: ATCC 3502

label_protocol: 1 ug of genomic DNA was labeled with Cy5 random primers and Klenow fragment


title: Ag-Mo-WG-G4122A: hyb 404


title: HSC_LRC_Rep3

description: Murine LRC HSC Replicate 3


title: Mbn2_Expression_Rep1


title: dCTCF Kc cells replicate 3 - Set 3

description: dCTCF ChIP-chip Kc cells

value: dCTCF


title: Kras_d26_rep2

description:
Gene expression data.
Replicate 2 of 2.


title: HSC_non-LRC_Rep2

description: Murine non-LRC HSC Replicate 2

value: Bone Marrow sorted for non-LRC CD34 Neg, Lin Neg, Sca1+, cKit+, CD150+, CD48 Neg, GFP Neg HSCs


title: Su(Hw) Kc cells replicate 3 - Set 3

description: Su(Hw) ChIP-chip Kc cells

value: Su(Hw)


title: Ag-Mo-WG-G4122A: hyb 2738

description: Transcriptome analysis of smooth muscle cells in atherosclerosis-prone and atherosclerosis-resistant regions of the aorta of C57Bl/6 mice at the age of 4 months

source_name: prone: aorta_arch_WT_pool_6

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit for dual color (Agilent) and the Cy5 CTP of Amersham. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy5 incorporation at 650 nm using a Nanodrop.

extract_protocol: Aorta were perfused with triton X-100 to remove endothelial cells. Aorta then divided into aortic arch (AA: aortic root, aortic arch, proximal 2 mm of thoracic aorta) and central thoracic aorta (TA: 6 mm distal from the proximal 2mm of the thoracic aorta). Aorta segments were immediately cut into small pieces and lysed in 350 µL Trizol reagent (Invitrogen, Merelbeke, Belgium). Subsequently, RNA was purified using the RNeasy MinElute kit (Qiagen, Antwerp, Belgium) and collected in 25 µL. RNA quality was tested by electrophoresis using the Agilent Bioanalyser. All RNA samples had a RNA integrity number (RIN) between 7.5 and 7.7. RNA extracts (12 µl) from the 6 mice were pooled and used for the microarray analysis.

value: C57Bl/6; 3 males, 3 females; age:16 weeks; tissue:aorta

source_name: resistant: thoracic_aorta_WT_pool_6

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit for dual color (Agilent) and the Cy3 CTP of Amersham. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy5 incorporation at 550 nm using a Nanodrop.


title: Su(Hw) Kc cells replicate 2 - Set 3

description: Su(Hw) ChIP-chip Kc cells

source_name: Input DNA from Kc cells


title: Ag-Mo-WG-G4122A: hyb 2739


title: dCTCF Kc cells replicate 1 - Set 3

description: dCTCF ChIP-chip Kc cells


title: Liver/Prostate_Red/Green_3

status: Public on May 14 2009

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

description: For a complete description of the columns in the supplemental array data files, see Molecular Devices's website for GenePixPro6.0, http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr

hyb_protocol: See Invitrogen Corp. website for NCode Human miRNA Microarray V3: http://tools.invitrogen.com/content/sfs/manuals/ncode_microarray_V3_man.pdf

scan_protocol: Slides were scanned using an Agilent microarray scanner G2505B instrument at 5 micron resolution. All scans were performed at 100% laser power, and all PMT settings were automatically adjusted.

data_processing: Images were processed and quantified using GenePix 4.0 software. The data were filtered (or flagged) on the basis of signal levels and spot quality.

source_name: FirstChoice Human Liver total RNA

label_protocol: See Invitrogen Corp. website for NCode miRNA Rapid Labeling System: http://tools.invitrogen.com/content/sfs/manuals/ncode_rapid_labeling_man.pdf

extract_protocol: Most RNA isolation protocols were developed for long messenger RNA and are not optimized to recover small molecules. Ambion has validated that our isolation procedures efficiently recover small RNA molecules and certify that these FirstChoice Total RNA products contain miRNA.

value: Liver

source_name: FirstChoice Human Prostate total RNA

value: Prostate


title: Liver/Prostate_Red/Green_1


title: Liver/Prostate_Green/Red_2


title: Liver/Prostate_Green/Red_3


title: Liver/Prostate_Green/Red_1


title: Liver/Prostate_Red/Green_2


title: Su(Hw) Kc cells replicate 1 - Set 3

description: Su(Hw) ChIP-chip Kc cells

source_name: Su(Hw) ChIP DNA from Kc cells


title: CDC657


title: dCTCF Kc cells replicate 2 - Set 3

description: dCTCF ChIP-chip Kc cells

source_name: dCTCF ChIP DNA from Kc cells


title: CDC42961


title: Prostate_3

hyb_protocol: See EXIQON website for miRCURY LNA microRNA Array kit v10.0 - human, mouse & rat: http://www.exiqon.com/array

label_protocol: See EXIQON website for miRCURY LNA microRNA Array Power Labeling kit: http://www.exiqon.com/SEEEMS/13442.asp


title: 73A


title: Prostate_2


title: Kc_Expression_Rep1


title: 69A


title: Liver_3


title: Prostate_2

hyb_protocol: See Ambion website mirVana Bioarrays: https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=603094

scan_protocol: Slides were scanned using an PerkinElmer ProScanArray instrument at 5 micron resolution. All scans were performed at 100% laser power and PMT 55.

label_protocol: See Ambion website for mirVana Labeling Kit: https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=603142


title: Prostate_1

extract_protocol: Total RNA prepared by Ambion (ABI). According to the manufacturer, RNA was prepared using a modified version of Ambion's ToTALLY RNA Kit for RNA isolation. Tissues were stored in RNAlater stabilization solution or frozen until processed. RNA was DNase-treated to minimize DNA contamination.


title: Liver_2


title: Liver_3


title: Liver_1

data_processing: Images were processed and quantified using GenePix 4.0 software (Axon Instruments, Union City, CA). The data were filtered (or flagged) on the basis of signal levels and spot quality.


title: Prostate_1

description: For a complete description of the columns in the supplemental array data files, see Agilent's Reference Guide for Feature Extraction Software v9.5, http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50416

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

data_processing: Agilent Feature Extraction v9.5.3, default miRNA parameters

label_protocol: Direct labeling with Cy3-pCp. See Agilent Technologies website for miRNA labeling protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500


title: Prostate_3


title: Liver_1


title: Prostate_2


title: Liver_2


title: Liver_1


title: Liver_3


title: Prostate_3


title: Liver_2


title: 62A


title: Prostate_1


title: CDC40234

tag: toxin sutbype


title: Adipose undernutrition in utero and during suckling rep3

first: Mary Elizabeth

last: Patti

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

description: Gene expression from epididymal fat of 3 week old male mouse, in utero undernutrition, undernutrition during suckling (UU)

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430A 2.0 array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data were analyzed using Affymetrix GCOS v.1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 1500.

source_name: epididymal fat

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.

growth_protocol: In utero 50% global food restriction (calculated based on pregnancy-day matched controls), followed by either ad lib feeding or continued 50% food restriction during suckling.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions.

value: ICR

tag: gender

value: Male

value: 3 weeks

tag: group assignment

value: UU

value: epididymal fat


title: Adipose undernutrition in utero and during suckling rep4

tag: tissue


title: Adipose undernutrition in utero and during suckling rep1


title: Adipose undernutrition in utero and during suckling rep2


title: Prostate_2

hyb_protocol: See TORAY website for 3D-Gene Human miRNA Oligo chip : http://www.3d-gene.com/products/pro_007.html

scan_protocol: Slides were scanned using an PerkinElmer ProScanArray instrument at 5 micron resolution. All scans were performed at 100% laser power and 3 times.

data_processing: Images were processed and quantified using GenePix 4.0 software (Axon Instruments, Union City, CA). The data were filtered (or flagged) on the basis of signal levels and spot quality. Each microarray, scanned at three times were merged into one.


title: Adipose utero undernutrition rep2

description: Gene expression from epididymal fat of 3 week old male mouse, in utero undernutrition, ad libitum chow during suckling (UC)

value: UC


title: Adipose utero undernutrition rep5


title: Adipose utero undernutrition rep1


title: Adipose utero undernutrition rep4


title: Adipose control rep5

description: Gene expression from epididymal fat of 3 week old male mouse, ad libitum chow in utero, ad libitum chow during suckling (CC)

value: CC


title: HSC_non-LRC_Rep1

description: Murine non-LRC HSC Replicate 1

value: SCL-tTA H2B-GFP transgenic mouse line that expresses the fusion protein histone H2B green fluorescent protein (H2B-GFP) under the control of a tetracycline responsive regulatory element, with the expression of the tTA-S2 transactivator under the control of the endogenous scl locus (SCL-tTA) limiting expression of GFP to both early embryonic and adult HSC/progenitor cells.


title: MDMs, hypoxia, rep2

city: Singapore

first: Subhra

last: Biswas

address: 8A Biomedical Grove

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Following fragmentation,  cRNA were hybridized on to Sentrix HumanRef-8_V2 Bead Chips from Illumina.

scan_protocol: Bead arrays were scanned using an llumina Bead Station 500X which employs SentrixScan Application V2.7.2 software.

data_processing:
Illumina BeadStudio software was used for quality control assessment and normalization of data conducted using the LOESS normalization method from BioConductor R packages.

Non-normalized data is available in the 'GSE16099_non-normalized_data.txt' file, which is linked to the GSE16099 record.

source_name: human MDMs subjected to severe hypoxia (< 0.1% O2)

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from 1 ug total RNA.

growth_protocol: Human Monocytes were isolated from Buffy coats and mononuclear cells was seeded in Iscove's Modified Dulbecco's Media  with 5% human AB serum  and 2mM L-Glutamine  and incubated at 37ºC, 5% CO2. After 2h, adherent monocytes were washed and cultured for 7 days to allow differentiation into MDMs.

extract_protocol: Total RNA was prepared using RNeasy kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Monocyte-derived macrophages (MDMs) were subjected to severe hypoxia (< 0.1% O2) or normoxia (20.9% O2) in 5% CO2 humidified multi-gas incubators for 18h.

value: blood

value: Human monocyte-derived macrophages


title: Transcriptome analysis of PNA+ and PNA- L. infantum promastigotes brep1

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

country: Spain

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

description: RNA INTEGRITY WAS CHECKED WITH AGILENT 6000 BIOANALYZER, USING AN RNA 6000 NANO CHIP

hyb_protocol: HYBRIDIZATION: prehybridization buffer with 0.1%BSA, 1.5 mg/ml polyT, 50% formamide and Cy3-/Cy5-labeled cDNAs; submerged in a water bath at 40ºC overnight.

scan_protocol: GENEPIX 6.0 SOFTWARE (AXON INSTRUMENTS)

data_processing:
ACQUISITION OF RAW DATA: GENEPIX 6.0 ANALYSIS TOOL
IMPORT *.GPR FILES TO ALMAZEN SOFTWARE (BIOALMA, TRES CANTOS, SPAIN)
NORMALIZATION BY LOWESS PER PIN METHOD WITH ALMAZEN SOFTWARE
THIS IS ONE OF THE THREE BIOLOGICAL REPLICATES. THE THREE REPLICATES WERE COMPARED BY T-TEST USING THE SAME SOFTWARE. SELECTION OF SPOTS WAS: Green/Red fluorescence intensity values >5000 FU respectively for Cy3 and Cy5. Fold change values >2 (Cy5/Cy3 if Cy5>Cy3) or <-2 (-Cy3/Cy5 if Cy5<Cy3). Selection by p-value <0.05

molecule: polyA RNA

organism: Leishmania infantum

source_name: culture, PNA+ PROCYCLIC PROMASTIGOTES isolate MCAN/ES/98/10445

label_protocol: INDIRECT METHOD: synthesis of aminoallyl-cDNA, degradation of RNA, purification of single-stranded cDNA, coupling of DMSO dissolved Cy3 dye in darkness for 1h and purification.

growth_protocol: RPMI 1640 (CAMBREX) supplemented with heat inactivated foetal bovine serum (CAMBREX) and penicillin /streptomycin (CAMBREX) 27ºC

extract_protocol:
TRIZOL REAGENT
PURIFICATION: RNeasy Minikit (ROCHE)
Total RNA was amplified with MESSAGE AMP II ARNA AMPLIFICATION KIT (AMBION), as only 1% of the population were PNA- promastigotes. Obviously, treatment for PNA+ promastigotes is the same as for PNA-.

treatment_protocol: Promastigotes from a stationary phase L. infantum culture were incubated with 50ug/ml peanut agglutinin (PNA) at room temperature for 30 min. Promastigotes in the sediment were resuspended in approximately 1ml supernatant and then were centrifuged at 200g. PNA+ promastigotes were on the pellet (optical microscopy: agglutinated promastigotes)

source_name: culture, PNA- METACYCLIC PROMASTIGOTES isolate MCAN/ES/98/10445

treatment_protocol: Promastigotes from a stationary phase L. infantum culture were incubated with 50ug/ml peanut agglutinin (PNA) at room temperature for 30 min. Promastigotes in the sediment were resuspended in approximately 1ml supernatant and then were centrifuged at 200g. PNA- promastigotes were in the supernatant, and were recovered by centrifugation at 2000g for 10 min (optical microscopy: non-agglutinated promastigotes, freely moving)


title: L188Q mutant LQ_1

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: transitently transfected with L 188Q mutant of surfactant protein C

hyb_protocol: accroding to manufacture's protocol (Affymetrix)

data_processing: MAS5 normalization, ANOVA

source_name: HEK293 cell line

tag: cell line


title: L188Q mutant LQ_3

scan_protocol: accroding to manufacture's protocol (Affymetrix)


title: Adipose utero undernutrition rep3


title: Delta Exon 4 mutant Ex4_3

description: transitently transfected with exon 4 mutant of surfactant protein C

label_protocol: accroding to manufacture's protocol (Affymetrix)


title: Delta Exon 4 mutant Ex4_1

extract_protocol: accroding to manufacture's protocol (Affymetrix)


title: L188Q mutant LQ_2


title: Prostate_1


title: Liver_2


title: Liver_1


title: MDMs, hypoxia, rep1


title: Transcriptome analysis of Leishmania infantum PNA+ procyclic and PNA- metacyclic promastigotes

tag: PNA+ PROCYCLIC PROMASTIGOTES isolate MCAN/ES/98/10445

tag: PNA- METACYCLIC PROMASTIGOTES isolate MCAN/ES/98/10445


title: Adipose control rep4


title: MDMs, normoxia, rep2

source_name: human MDMs subjected to normoxia (20.9% O2)


title: Transcriptome analysis of PNA+ and PNA- L. infantum promastigotes brep2


title: Prostate_3


title: Liver_3


title: MDMs, normoxia, rep1


title: Adipose control rep2


title: Adipose control rep1


title: Adipose control rep3


title: Delta Exon 4 mutant EX4_2


title: Wild-type control 197_3

description: transitently transfected with wild-type surfactant protein C


title: Wild-type control 197_2


title: Wild-type control 197_1


title: Moroc9-75_5d_rep3

status: Public on May 13 2009

city: Aleppo

first: Michael

last: Baum

state: Aleppo

address: ICARDA

department: BIGMP

country: Syria

institute: ICARDA

description: All scanned data from barley 1 GeneChips were processed by robust multiarray average (RMA) (Irizarry et al., 2003) using ArrayAssist software version 3.4 (Stratagene, La Jolla, CA, UAS)

hyb_protocol: Biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length, and 15 µg of fragmented cRNA was used for each hybridization. Barley 1 GeneChips were hybridized for 16 h at 45°C with rotation in a GeneChip® Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with R-phycoerythrin streptavidin in a Fluidics Station.

scan_protocol: The Arrays were subsequently scanned with Affymetrix GeneChip® Scanner 3000

data_processing:
Normalized expression values were computed from raw CEL files by first applying the RMA model of probe-specific correction of perfect match probes. The algorithm consists of three steps—a model-based background correction stage neutralizes the effects of background noise and the processing artifacts, a subsequent quantile normalization stage aligns expression values to a common scale, and finally, an iterative median polishing procedure summarizes the data and generates a single expression value for each probe set. Resulting RMA expression values were log2-transformed. Average log signal intensity values of three biological replicates for each sample were then computed and these were used for further analysis.  To identify differentially expressed genes, student's t-test was applied with a maximal FDR (false discovery rate) of 5% (Benjamini-Hochberg algorithm).
RMA data for each individual Affymetrix chip not available. Thus the Sample data tables instead report MAS5.0-processed data.  A table of the average, log2 RMA signal intensity values of three biological replicates for each sample is linked as a supplementary file on the GSE15970 record.

organism: Hordeum vulgare

source_name: Flag leaves, harvested at 5 d after drought stress

label_protocol: 5 µg of high quality total RNA were reverse transcribed using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA, USA). The resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using Affymetrix IVT Labeling Kit as Expression Analysis Technical Manual (2001, Affymetrix)

extract_protocol: Seven flag leaves of a replication for each genotype were harvested at 5 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).

tag: genotype

tag: trait for drought tolerance

value: drought tolerance (sensitive)

value: flag leaves

tag: treatment

value: 5 d after drought stress


title: Moroc9-75_3d_rep2

source_name: Flag leaves, harvested at 3 d after drought stress

extract_protocol: Seven flag leaves of a replication for each genotype were harvested at 3 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).

value: 3 d after drought stress


title: Moroc9-75_3d_rep1


title: Moroc9-75_1d_rep1

source_name: Flag leaves, harvested at 1 d after drought stress

extract_protocol: Seven flag leaves of a replication for each genotype were harvested at 1 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).

value: 1 d after drought stress


title: Moroc9-75_0d_rep3

source_name: Flag leaves, harvested at 0 d after drought stress

extract_protocol: Seven flag leaves of a replication for each genotype were harvested at 0 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).

value: 0 d after drought stress


title: Moroc9-75_5d_rep2


title: Moroc9-75_1d_rep3


title: Moroc9-75_0d_rep2


title: Moroc9-75_5d_rep1


title: Moroc9-75_0d_rep1


title: HS41-1_5d_rep2

value: drought tolerance


title: HS41-1_5d_rep3


title: HS41-1_1d_rep1


title: HS41-1_3d_rep2


title: HS41-1_3d_rep1


title: HS41-1_0d_rep3


title: HS41-1_1d_rep2


title: HS41-1_5d_rep1


title: HS41-1_3d_rep3


title: HS41-1_1d_rep3


title: Martin_5d_rep2

value: Martin


title: HS41-1_0d_rep1


title: Martin_3d_rep1


title: Martin_1d_rep2


title: Embryo at Day 1, female biological replicate 9

city: kansas city

first: Sachin

last: Mathur

state: MO

address: 5100 Rockhill Drive

department: School of Computing & Engineering

institute: University of Missouri Kansas City

description: chicken embryo at 1 day old

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Standard Affymetrix Scanner

data_processing: The data were analyzed with MAS5 data processing method implemented in Bioconductor-Affy package with 100 as target intensity.

organism: Gallus gallus

source_name: Female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50ng total RNA.

growth_protocol: HH stage 4- chicken embryos were dissected out of eggs and put on EC culture in humidified incubator for 3 hours at 380C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Primitive streak tissues (400umx400um at 70% to 90% streak level) were dissected out using tungsten needle under dissecting microscope. Tissues were then rinsed in ice cold Tyrode's solution and transfered into the Trizol solution (GibcoBRL). Then they were frozen immediately on dry ice and stored at -80 degrees.

value: Embryo

tag: developmental stage

value: Hamburger-Hamilton stage 4

tag: sex

value: Female

tag: age

value: 1 day


title: HS41-1_0d_rep2


title: Embryo at Day 1, male biological replicate 6

description: chicken embryo at 1 day old

source_name: Male

value: Male


title: Embryo at Day 1, male biological replicate 8

description: chicken embryo at 1 day old


title: Martin_5d_rep1


title: Embryo at Day 1, male biological replicate 9

description: chicken embryo at 1 day old


title: Martin_1d_rep3


title: Martin_3d_rep3


title: Embryo at Day 1, male biological replicate 7

description: chicken embryo at 1 day old


title: Martin_5d_rep3


title: Embryo at Day 1, female biological replicate 8

description: chicken embryo at 1 day old


title: Embryo at Day 1, male biological replicate 5

description: chicken embryo at 1 day old


title: Martin_3d_rep2


title: Embryo at Day 1, female biological replicate 7

description: chicken embryo at 1 day old


title: Embryo at Day 1, female biological replicate 4

description: chicken embryo at 1 day old


title: Embryo at Day 1, male biological replicate 3

description: chicken embryo at 1 day old


title: Embryo at Day 1, female biological replicate 5

description: chicken embryo at 1 day old


title: Embryo at Day 1, female biological replicate 6

description: chicken embryo at 1 day old


title: Embryo at Day 1, male biological replicate 4

description: chicken embryo at 1 day old


title: Martin_1d_rep1


title: Martin_0d_rep3


title: Embryo at Day 1, male biological replicate 2

description: chicken embryo at 1 day old


title: Embryo at Day 1, female biological replicate 3

description: chicken embryo at 1 day old


title: Root_Hg2

city: Texcoco

first: Marta

middle: Silva

last: Lopes

state: Mexico

address: km 45, carretera Mexico-Veracruz, El Batan, Texcoco

department: wheat physiology

country: Mexico

institute: cimmyt

description: All sample extraction and micro chip manipulation were carried out at PROGENIKA, in SPAIN (Bilbao)

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Normalization was carried out in 2 steps: using GeneSpring v7.1 (Agilent) and previously scaled with GCOS.

source_name: Barley roots exposed to 1000 uM Hg

label_protocol: Standard Affymetrix procedures.

growth_protocol: Barley (Hordeum vulgare L. cv. Graphic) seeds were carefully chosen with similar weight, shape and size and sown in 1 L pots containing sand in a glasshouse for 15 days (Experimental Fields of the University of Barcelona) and irrigated with a half strength Hoagland solution containing either 0 µM (control), 500 µM or 1000 µM of HgCl2. Daily means of temperature, relative humidity and maximum irradiance in the glasshouse throughout the experiment were 16ºC, 45% and 378 Wm-2, respectively. For root and shoot dry weight, 5 plantlets were sampled, immediately frozen in liquid nitrogen, lyophylized and dry weights were recorded and shoot to root ratio calculated. Additional three plantlets per treatment (only controls and 1000 μM HgCl2) were sampled and the entire roots were separated from leaves, washed with de-ionized water and immediately frozen in liquid N and kept at -80ºC until use for RNA extractions.

extract_protocol: Trizol reagent and Rneasy Quiagen

value: root

tag: agent


title: Root_Control3

source_name: Barley roots grown in control conditions

value: control


title: Root_Control2


title: Embryo at Day 1, male biological replicate 1

description: chicken embryo at 1 day old


title: Control in vivo - 2

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description:
RNA from fathead minnow control ovary
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)

scan_protocol: The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA)

data_processing: The intensity of each spot was summarized by the median pixel intensity. A log2 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

organism: Pimephales promelas

source_name: Fathead minnow control ovary

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)

growth_protocol: Adult (ca. 6 month old) female FHM from an on-site culture (EPA’s Mid-Continent Ecology Division Laboratory, Duluth) were acclimated to test conditions (25oC, 16:8 light:dark photoperiod, and fed adult brine shrimp twice daily) over a period of one week as described in USEPA (2001).  Exposures were initiated by transferring fish from the acclimation tanks to randomly assigned treatment tanks, n = 6 fish per treatment tank.  Water quality conditions, monitored daily, were maintained within the guidelines established for fathead minnow reproduction tests.

extract_protocol: Total RNA was isolated from gonadal tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Fathead minnow ovary exposed in vitro for 12h to fadrozole, or solvent control

value: ovary

source_name: Reference sample

tag: sample type

value: liver, brain, and gonad pool


title: FAD in vivo - 1

description:
RNA from fathead minnow ovary exposed in vivo to a 50 ug/L fadrozole
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

source_name: Fathead minnow ovary exposed to fadrozole


title: Martin_0d_rep1


title: Embryo at Day 1, female biological replicate 1

description: chicken embryo at 1 day old


title: Control in vivo - 4


title: FAD in vivo - 2